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Schmidt M, Avagyan S, Reiche K, Binder H, Loeffler-Wirth H. A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections. Curr Issues Mol Biol 2024; 46:4701-4720. [PMID: 38785552 PMCID: PMC11119626 DOI: 10.3390/cimb46050284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
A crucial feature of life is its spatial organization and compartmentalization on the molecular, cellular, and tissue levels. Spatial transcriptomics (ST) technology has opened a new chapter of the sequencing revolution, emerging rapidly with transformative effects across biology. This technique produces extensive and complex sequencing data, raising the need for computational methods for their comprehensive analysis and interpretation. We developed the ST browser web tool for the interactive discovery of ST images, focusing on different functional aspects such as single gene expression, the expression of functional gene sets, as well as the inspection of the spatial patterns of cell-cell interactions. As a unique feature, our tool applies self-organizing map (SOM) machine learning to the ST data. Our SOM data portrayal method generates individual gene expression landscapes for each spot in the ST image, enabling its downstream analysis with high resolution. The performance of the spatial browser is demonstrated by disentangling the intra-tumoral heterogeneity of melanoma and the microarchitecture of the mouse brain. The integration of machine-learning-based SOM portrayal into an interactive ST analysis environment opens novel perspectives for the comprehensive knowledge mining of the organization and interactions of cellular ecosystems.
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Affiliation(s)
- Maria Schmidt
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
| | - Susanna Avagyan
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan Str., Yerevan 0062, Armenia
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstrasse 1, 04103 Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, 04103 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan Str., Yerevan 0062, Armenia
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
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Liao YM, Hsu SH, Chiou SS. Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies. Int J Mol Sci 2024; 25:2416. [PMID: 38397092 PMCID: PMC10889174 DOI: 10.3390/ijms25042416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Chimeric antigen receptor (CAR)-T-cell therapy has greatly improved outcomes for patients with relapsed or refractory hematological malignancies. However, challenges such as treatment resistance, relapse, and severe toxicity still hinder its widespread clinical application. Traditional transcriptome analysis has provided limited insights into the complex transcriptional landscape of both leukemia cells and engineered CAR-T-cells, as well as their interactions within the tumor microenvironment. However, with the advent of single-cell sequencing techniques, a paradigm shift has occurred, providing robust tools to unravel the complexities of these factors. These techniques enable an unbiased analysis of cellular heterogeneity and molecular patterns. These insights are invaluable for precise receptor design, guiding gene-based T-cell modification, and optimizing manufacturing conditions. Consequently, this review utilizes modern single-cell sequencing techniques to clarify the transcriptional intricacies of leukemia cells and CAR-Ts. The aim of this manuscript is to discuss the potential mechanisms that contribute to the clinical failures of CAR-T immunotherapy. We examine the biological characteristics of CAR-Ts, the mechanisms that govern clinical responses, and the intricacies of adverse events. By exploring these aspects, we hope to gain a deeper understanding of CAR-T therapy, which will ultimately lead to improved clinical outcomes and broader therapeutic applications.
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Affiliation(s)
- Yu-Mei Liao
- Division of Hematology-Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Hsien Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shyh-Shin Chiou
- Division of Hematology-Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Derraz B, Breda G, Kaempf C, Baenke F, Cotte F, Reiche K, Köhl U, Kather JN, Eskenazy D, Gilbert S. New regulatory thinking is needed for AI-based personalised drug and cell therapies in precision oncology. NPJ Precis Oncol 2024; 8:23. [PMID: 38291217 PMCID: PMC10828509 DOI: 10.1038/s41698-024-00517-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/06/2024] [Indexed: 02/01/2024] Open
Abstract
Until recently the application of artificial intelligence (AI) in precision oncology was confined to activities in drug development and had limited impact on the personalisation of therapy. Now, a number of approaches have been proposed for the personalisation of drug and cell therapies with AI applied to therapy design, planning and delivery at the patient's bedside. Some drug and cell-based therapies are already tuneable to the individual to optimise efficacy, to reduce toxicity, to adapt the dosing regime, to design combination therapy approaches and, preclinically, even to personalise the receptor design of cell therapies. Developments in AI-based healthcare are accelerating through the adoption of foundation models, and generalist medical AI models have been proposed. The application of these approaches in therapy design is already being explored and realistic short-term advances include the application to the personalised design and delivery of drugs and cell therapies. With this pace of development, the limiting step to adoption will likely be the capacity and appropriateness of regulatory frameworks. This article explores emerging concepts and new ideas for the regulation of AI-enabled personalised cancer therapies in the context of existing and in development governance frameworks.
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Affiliation(s)
- Bouchra Derraz
- ProductLife Group, Paris, France
- Groupe de recherche et d'accueil en droit et économie de la santé (GRADES), Faculty of Pharmacy, University Paris-Saclay, Paris, France
| | | | - Christoph Kaempf
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Franziska Baenke
- Carl Gustav Carus University Hospital Dresden, Dresden University of Technology, Dresden, Germany
| | - Fabienne Cotte
- Department of Emergency Medicine, University Clinic Marburg, Philipps-University, Marburg, Germany
| | - Kristin Reiche
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig, Germany
- Institute of Clinical Immunology, University Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, University Leipzig, Leipzig, Germany
| | - Jakob Nikolas Kather
- Carl Gustav Carus University Hospital Dresden, Dresden University of Technology, Dresden, Germany
- Else Kröner Fresenius Center for Digital Health, TUD Dresden University of Technology, Dresden, Germany
| | - Deborah Eskenazy
- Groupe de recherche et d'accueil en droit et économie de la santé (GRADES), Faculty of Pharmacy, University Paris-Saclay, Paris, France
| | - Stephen Gilbert
- Carl Gustav Carus University Hospital Dresden, Dresden University of Technology, Dresden, Germany.
- Else Kröner Fresenius Center for Digital Health, TUD Dresden University of Technology, Dresden, Germany.
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Tang L, Huang ZP, Mei H, Hu Y. Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer. Mil Med Res 2023; 10:52. [PMID: 37941075 PMCID: PMC10631149 DOI: 10.1186/s40779-023-00486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023] Open
Abstract
Advances in chimeric antigen receptor (CAR)-T cell therapy have significantly improved clinical outcomes of patients with relapsed or refractory hematologic malignancies. However, progress is still hindered as clinical benefit is only available for a fraction of patients. A lack of understanding of CAR-T cell behaviors in vivo at the single-cell level impedes their more extensive application in clinical practice. Mounting evidence suggests that single-cell sequencing techniques can help perfect the receptor design, guide gene-based T cell modification, and optimize the CAR-T manufacturing conditions, and all of them are essential for long-term immunosurveillance and more favorable clinical outcomes. The information generated by employing these methods also potentially informs our understanding of the numerous complex factors that dictate therapeutic efficacy and toxicities. In this review, we discuss the reasons why CAR-T immunotherapy fails in clinical practice and what this field has learned since the milestone of single-cell sequencing technologies. We further outline recent advances in the application of single-cell analyses in CAR-T immunotherapy. Specifically, we provide an overview of single-cell studies focusing on target antigens, CAR-transgene integration, and preclinical research and clinical applications, and then discuss how it will affect the future of CAR-T cell therapy.
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Affiliation(s)
- Lu Tang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Zhong-Pei Huang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China.
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China.
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Pierzynowska K, Gaffke L, Zaucha JM, Węgrzyn G. Transcriptomic Approaches in Studies on and Applications of Chimeric Antigen Receptor T Cells. Biomedicines 2023; 11:biomedicines11041107. [PMID: 37189725 DOI: 10.3390/biomedicines11041107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Chimeric antigen receptor T (CAR-T) cells are specifically modified T cells which bear recombinant receptors, present at the cell surface and devoted to detect selected antigens of cancer cells, and due to the presence of transmembrane and activation domains, able to eliminate the latter ones. The use of CAR-T cells in anti-cancer therapies is a relatively novel approach, providing a powerful tool in the fight against cancer and bringing new hope for patients. However, despite huge possibilities and promising results of preclinical studies and clinical efficacy, there are various drawbacks to this therapy, including toxicity, possible relapses, restrictions to specific kinds of cancers, and others. Studies desiring to overcome these problems include various modern and advanced methods. One of them is transcriptomics, a set of techniques that analyze the abundance of all RNA transcripts present in the cell at certain moment and under certain conditions. The use of this method gives a global picture of the efficiency of expression of all genes, thus revealing the physiological state and regulatory processes occurring in the investigated cells. In this review, we summarize and discuss the use of transcriptomics in studies on and applications of CAR-T cells, especially in approaches focused on improved efficacy, reduced toxicity, new target cancers (like solid tumors), monitoring the treatment efficacy, developing novel analytical methods, and others.
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jan M. Zaucha
- Department of Hematology and Transplantology, Medical University of Gdansk, Smoluchowskiego 17, 80-214 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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